Abstract Background The evidence that cardiovascular disease begins in childhood and adolescence, especially in the presence of excess weight, is associated with dysfunction on adipokine pro-inflammatory secretion. These affect glucose metabolism and lead to other complications related to insulin resistance and cardiovascular disease. This study assessed the association of anthropometric and metabolic parameters related to obesity, cardiovascular risk, and insulin resistance with concentrations of resistin and visfatin, in children. Methods A cross-sectional study was developed with 178 children of 6–10 years old enrolled in public city schools. Anthropometric data, composition body, clinical, and biochemical were measured according to standard procedures. We used multiple regression models by stepwise method to evaluate the associations of resistin and visfatin with variables of interest. Results In healthy weight children, resistin was associated with LDL cholesterol, visfatin, atherogenic index, and waist-to-height ratio, whereas in obese children resistin was associated with visfatin and interaction between conicity index and HOMA-AD. Furthermore, in healthy weight children, visfatin was associated to resistin and triceps skinfold thickness and negatively associated to HOMA-AD, while in obese ones visfatin was associated with waist-to-height ratio, atherogenic index, resistin, and interaction between trunk adiposity index and adiponectin and was negatively associated with the HOMA-IR index. Conclusions Our study shows an association between anthropometric and biochemical variables related to visceral fat and inflammation. These results suggest the resistin and visfatin as good pro-inflammatory markers. In addition, both adipokines are strongly related to central obesity, in children.